Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Either with Package.get_packages_files(codebase) to get the files of a
package in a codebase, or with get_files_for_packages(codebase) to list
all the files and the package_uid they belong to.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

This way it is possible to focus a scan only on some packages types
and not always boil the ocean.

For this we now have two lists of DatafileHandlers: one for system
packages and one for application packages.

The new UX is to have a change in the command line options:
--package detects only application packages (which basically is what it
was doing in the previous release)
--system-package is new and detects only system packages.
These two options can be combined to detect all package types.

Several functions now accept new "application=True, system=False"
arguments


Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

The new commoncode.resource has an efficient get_resource() function
to lookup a resource by path.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Always strip leading and trailing slahes from paths.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Also set the correct output format version to 2.0. The latest version
was 1.0

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Use instead Resource.has_parent()

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Thete are new path prefixes added to each merged codebase

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

We need to adopt a different approach when a codebase has a single
resource and when the scan is done with "strip_root" which is a common
case in tests.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

* Also use the --system-package option correctly

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

* Also use the --system-package option correctly
* Remove/rename dangling JSON expected test results file

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

AlpineInstalledDatabaseHandler.parse was making an incorrect call and
was not tested. This is now tested with a mock rootfs extracted from
a recent Alpine docker image and called correctly.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

resourec.parent can be null so we better guard against this.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Until the beta cycle is completed

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

- Ensure we correctly dela with installed RPM dbs in
  BaseRpmInstalledDatabaseHandler.parse() and
  BaseRpmInstalledDatabaseHandler.assemble() with the new commoncode.
  In particular lookup the Codebase Resources by path directly
  and properly search and tag file_references and
  missing_file_references.

- Add en to end test with a mock Fedora rootfs
- Add minimal, incomplete support for RPM distros in distro.py

- and other misc. code formatting and minor documentation updates.

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>

Signed-off-by: Philippe Ombredanne <pombredanne@nexb.com>